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        <title>Gap filling - Peak finder</title>
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        <h1>Peak finder</h1>

        <h2>Description</h2>
        <p>
            Following alignment, the resulting peak list may contain missing
            peaks as a product of a deficient peak detection or a mistake in the alignment of
            different peak lists.
		</p>
		
		<p>
            The fact that one peak is missing after the alignment does not imply that the
            peak does not exits. In most cases it is present but was undetected by the
            previous algorithms.
        </p>

        <p>
            This algorithm fills the gaps in the peak list when it is possible according with the parameters
            defined by the user.
            The most crucial parameters are "m/z tolerance" and "RT tolerance" which define the window where
            the algorithm should find the new peak. It is centered in the m/z average and retention time average of
            the source peak list. Once the best candidate is found inside the window, its intensity and its shape in RT direction is also
            checked.
		</p>
		
		<p>
            It can also add a previous correction of the retention time in the case it is needed. It will
            change the position of the defined window depending on the prediction of a RT model created
            using all the already aligned peaks in each pair.
        </p>

        <h4>RT correction</h4>
        <p>
            When RT correction is applied, the algorithm is divided in two main steps. In the first step,
            one random sample is taken from the multiple peak list and is used as a master list. All the gaps of this master list are filled using all the others samples.
            For each pair of samples the algorithm creates a model of the retention time.
            In the second step the master list is used to fill the gaps of the rest of the samples,
            creating also a retention time model for each pair (as is is showed in the figure below).

        </p>

        <p>
            <img src="gapfilling.png" name="scheme">
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        <h4>Method parameters</h4>

        <dl>
            <dt>Name suffix</dt>
            <dd>Suffix to be added to the peak list name.</dd>

            <dt>Intensity tolerance</dt>
            <dd>This value sets the maximum allowed deviation from expected shape of a peak
                in chromatographic direction.</dd>

            <dt>M/Z tolerance</dt>
            <dd>This value sets the range, in terms of m/z, to search for possible peak in the raw
                data. Maximum allowed m/z difference.</dd>

            <dt>Retention time tolerance type</dt>
            <dd>Its value can be relative or absolute. The next parameters should be fill depending
                on the value chosen in this parameter. </dd>

            <dt>Absolute RT tolerance</dt>
            <dd>This value sets the range, in terms of retention time, to search for possible peak in the raw
                data. Maximum allowed absolute RT difference.</dd>

            <dt>Relative RT tolerance</dt>
            <dd>This value sets the range, in terms of retention time, to search for possible peak in the raw
                data. Maximum allowed relative RT difference.</dd>

            <dt>RT Correction</dt>
            <dd>When it is checked, correction of the retention time will be applied to avoid the problems caused by the deviation
                of the retention time between the samples.</dd>

        </dl>
        
        
        <p>
        New peak list showing the filled peaks with a yellow mark.<br>
        <img src="gapfillingResult.png" name="gap filling result">
        </p>

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